/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

#include <iostream>

#include "itkBioGenome.h"
#include "itkMath.h"


int
itkBioGenomeTest(int, char *[])
{
  itk::bio::Genome genome;


  genome.InsertGene("Tubulin");
  genome.InsertGene("Cyclin");

  const double tolerance = 1e-16;

  constexpr double inLevel = 0.74;
  genome.SetExpressionLevel("Cyclin", inLevel);

  const double outLevel = genome.GetExpressionLevel("Cyclin");

  if (itk::Math::abs(inLevel - outLevel) / outLevel > tolerance)
  {
    std::cerr << "Error in SetExpressionLevel()/GetExpressionLevel()" << std::endl;
    return EXIT_FAILURE;
  }

  genome.KnockOutGene("Cyclin");

  if (itk::Math::abs(genome.GetExpressionLevel("Cyclin")) > tolerance)
  {
    std::cerr << "Error in KnockOutGene()/GetExpressionLevel()" << std::endl;
    return EXIT_FAILURE;
  }

  constexpr double value = 3.0;
  constexpr double threshold = 2.0;
  constexpr double slant = 5.0;

  const double sigmoid = itk::bio::Genome::Sigmoide(threshold, slant, value);

  const double expectedSigmoid = std::atan((value - threshold) / slant) / 3.1416 + 0.5001;

  if (itk::Math::abs(sigmoid - expectedSigmoid) / expectedSigmoid > tolerance)
  {
    std::cerr << "Error in Sigmoid()" << std::endl;
    std::cerr << "Expected valued = " << expectedSigmoid << std::endl;
    std::cerr << "Computed valued = " << sigmoid << std::endl;
    std::cerr << "Difference      = " << (sigmoid - expectedSigmoid) << std::endl;
    std::cerr << "Tolerance       = " << tolerance << std::endl;
    return EXIT_FAILURE;
  }


  constexpr double cyclinLevel = 3.45;
  constexpr double tubulinLevel = 2.79;

  genome.SetExpressionLevel("Cyclin", cyclinLevel);
  genome.SetExpressionLevel("Tubulin", tubulinLevel);

  itk::bio::Genome genome2;

  genome2.Copy(genome);

  if (itk::Math::abs(genome.GetExpressionLevel("Tubulin") - genome2.GetExpressionLevel("Tubulin")) > tolerance)
  {
    std::cerr << "Error in Copy()" << std::endl;
    return EXIT_FAILURE;
  }

  if (itk::Math::abs(genome.GetExpressionLevel("Cyclin") - genome2.GetExpressionLevel("Cyclin")) > tolerance)
  {
    std::cerr << "Error in Copy()" << std::endl;
    return EXIT_FAILURE;
  }

  std::cout << "Test Passed !" << std::endl;
  return EXIT_SUCCESS;
}
